Interesting post! I read Paper Towns first, and without an awareness of Green's infamy for MPDG. And I found it to be a stellar example of a MPDG nevertheless: Margo is absent for most of the novel; she provides motivation for the male characters but her needs are subordinated through the text; the novel ends somewhat inexplicably with the promise of a romantic relationship between her and Q. I think Green's awareness of these issues encourages me a bit (and I need to read TFioS, but I'm avoiding it right now for trigger issues), but I'm not sure that I feel that Paper Towns really addressed these issues so much as perpetuating them despite his awareness of them.

But your emotions are fascinating and interesting.